/*
 * University of Illinois Open Source License
 * Copyright 2007 Luthey-Schulten Group, 
 * All rights reserved.
 * 
 * Developed by: Luthey-Schulten Group
 * 			     University of Illinois at Urbana-Champaign
 * 			     http://www.scs.illinois.edu/~schulten
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a copy of
 * this software and associated documentation files (the Software), to deal with 
 * the Software without restriction, including without limitation the rights to 
 * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
 * of the Software, and to permit persons to whom the Software is furnished to 
 * do so, subject to the following conditions:
 * 
 * - Redistributions of source code must retain the above copyright notice, 
 * this list of conditions and the following disclaimers.
 * 
 * - Redistributions in binary form must reproduce the above copyright notice, 
 * this list of conditions and the following disclaimers in the documentation 
 * and/or other materials provided with the distribution.
 * 
 * - Neither the names of the Luthey-Schulten Group, University of Illinois at
 * Urbana-Champaign, nor the names of its contributors may be used to endorse or
 * promote products derived from this Software without specific prior written
 * permission.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL 
 * THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 
 * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
 * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
 * OTHER DEALINGS WITH THE SOFTWARE.
 *
 * Author(s): Elijah Roberts
 */

#include <stdio.h>
#include <stdlib.h>
#include "symbol.h"
#include "ShortIntList.h"
#include "alphabet.h"
#include "alignedSequence.h"
#include "sequenceAlignment.h"
#include "fastaWriter.h"


/**
 * This method writes a sequence alignment out as a FASTA file.
 *
 * @param   filename    The name of the file to write the alignment out as.
 * @param   alignment   The sequence alignment to write out.
 * @param   lineLength  The maximum number of residues on a single line. (default=60)
 * @return  1 on success, o on error.
 */
bool FASTAWriter::writeSequenceAlignment(const char* filename, SequenceAlignment* alignment, int lineLength)
{
   int i, j;
    //Open the file.
    FILE* fp = fopen(filename,"w");
    if (fp == NULL) return false;
    
    //Go through each sequence in the alignment.
    for (i=0; i<alignment->getNumberSequences(); i++)
    {    
        //Get the sequence.
        AlignedSequence* sequence = alignment->getSequence(i);
        
        //Write out the sequence.
        fprintf(fp, ">%s\n", sequence->getName());
        for (j=0; j<sequence->getSize(); j++)
        {
            if (j > 0 && j%lineLength == 0) fprintf(fp, "\n");
            fprintf(fp, "%c", sequence->get(j).getOne());
        }
        fprintf(fp, "\n");
    }

    //Close the file.
    fclose(fp);
    
    return true;
}
